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eROSA Stakeholder WS1: AgroPortal: a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition

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eROSA Stakeholder WS1: AgroPortal: a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition

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Presentation by Clément Jonquet delivered at the 1st eROSA Stakeholder Workshop in Montpellier, 6/7/2017

Presentation by Clément Jonquet delivered at the 1st eROSA Stakeholder Workshop in Montpellier, 6/7/2017

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eROSA Stakeholder WS1: AgroPortal: a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition

  1. 1. AgroPortal a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition Clément Jonquet jonquet@lirmm.fr eRosa stakeholder workshop Montpellier, July 6th 2017 http://agroportal .lirmm.fr
  2. 2. Working with vocabularies & ontologies – a portal please! • You’ve built an ontology, how do you let the world know? • You need an ontology, where do you go to get it? • How do you know whether an ontology is any good? • How do you find data that are relevant to the domain of the ontology (or to specific terms)? • How could you use ontologies without managing them ? 2AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  3. 3. Objectives of AgroPortal project • Develop and support a reference ontology repository for agronomy • Primary focus on agronomy • One-stop-shop for agronomical ontologies & services • Reusing the NCBO BioPortal technology • Avoid to re-implement what has been done, facilitate interoperability • Reusing the scientific outcomes, experience & methods of biomedicine • Enable cross domain interaction • Enable straightforward use of agronomical ontologies • Respect the requirements of the agronomic community • Fully semantic web compliant infrastructure • Focus on new enabled science 3AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  4. 4. 5 Driving Agronomic Use Cases ➢ IBC Rice Genomics & AgroLD project ➢ Data integration and knowledge management related to rice (P. Larmande) ➢ RDA Wheat Data Interoperability working group ➢ Common framework for publishing wheat data (E. Dzalé-Yeumo) ➢ LovInra : INRA Linked Open Vocabularies ➢ Vocabularies produced by INRA scientists (S. Aubin) ➢ Crop Ontology project ➢ Ontologies for describing crop germplasm & traits (E. Arnaud) ➢ GODAN global map of agri-food data standards ➢ VEST/AgroPortal MAP of standards (V. Pesce) 4AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  5. 5. AgroPortal: a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition Publish, search, download Browse, visualize Peer review Versioning Annotation Recommendati on Mapping Notes Projects 64 ontologies, 95 candidates 5 driving use cases ~60 registered users http://agroportal. lirmm.fr 5
  6. 6. Describe ontologies with semantic metadata Display “per ontology” Ontology specific properties => viewable and editable within the ontology specific page Display “per property” Global presentation of the properties Synthesis diagrams & listing 6
  7. 7. Examples of ontologies uploaded in AgroPortal Title Format Groups Size IBP Rice Trait Ontology (CO_320) OWL CROP, RICE ~2K IBP Wheat Trait Ontology (CO_321) OWL CROP, WHEAT ~1K IBP Wheat Anatomy Ontology (CO_121) OBO CROP, WHEAT ~80 IBP Crop Research (CO_715) OBO CROP ~250 Multi-Crop Passport Ontology (CO_020) OBO CROP ~90 Biorefinery (BIOREFINERY) OWL LOVINRA ~300 Matter Transfer (TRANSMAT) OWL LOVINRA ~1.1K Plant Ontology (PO) OWL WHEAT, RICE, OBOF ~2K Plant Trait Ontology (TO) OWL WHEAT, RICE, OBOF ~4.4K Durum Wheat (DURUM_WHEAT) OWL LOVINRA ~130 Agricultural Experiments (AEO) OWL LOVINRA ~60 Environment Ontology (ENVO) OWL WHEAT, OBOF ~6.3K NCBI Organismal Classification (NCBITAXON) RRF WHEAT ~900K AnaEE Thesaurus (ANAEE) SKOS LOVINRA ~3.3K French Crop Usage (CROPUSAGE) SKOS none ~300 Agrovoc (AGROVOC) SKOS none ~32K Food Ontology (FOODON) OWL OBOF ~10K National Agriculture Library Thesaurus (NALT) SKOS none ~67K Global Agricultural Concept Scheme (GACS) SKOS none ~585K 7AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  8. 8. Ontology groups and categories 8 Category Number Plant Phenotypes and Traits 18 Plant Anatomy and Development 3 Natural Resources, Earth and Environment 2 Animal Science and Animal Products 6 Agricultural Research, Technology and Engineering 9 Breeding and Genetic Improvement 1 Plant Science and Plant Products 4 Plant Genetic Resources 2 Food and Human Nutrition 4 Taxonomic Classifications of Organisms 2 Farms and Farming Systems 3 Specific slices display to use only the ontologies of a group http://inra.agroportal.lirmm.fr/ AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  9. 9. Align ontologies one another concept by concept 9
  10. 10. AgroPortal Annotator identifies ontology concepts within plain text for semantic indexing 10
  11. 11. AgroPortal Recommender get the most relevant ontologies for your data 11
  12. 12. AgroPortal landscape page Display “per property” • Global presentation of the properties • Synthesis diagrams & listing • Allows to explore the agronomical ontology landscape by automatically aggregating the metadata fields of each ontologies in explicit vizualizations (charts, term cloud and graphs). 12AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  13. 13. REST API http://data.agroportal.lirmm.fr/documentation SPARQL endpoint http://sparql.agroportal.lirmm.fr/test 13AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  14. 14. Long term vision… 14AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  15. 15. 2017-2019 • Maintain the current prototype as a “community builder” • Harvest, harvest, harvest…. Share, share, share… demonstrate • Ontologies, Mappings, Metadata • Harmonize (metadata) with Map of Standards, BioSharing 15AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  16. 16. 2020-2025 • EOSC Services vision • Harmonization of the vocabularies and ontologies • Reuse • Semantic richness (not just thesaurus) • Endorsement of GACS as a pivot vocabulary • Thesaurus (the terms) • Upper level ontologies (high level semantics) • Connected to domain specific ontologies 16AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  17. 17. 2020-2025 (following) • Help the community to adopt semantic Web / W3C standards to describe their standards • No more PDF standard descriptions • Data, data, data…. annotations, data-lifting, etc. AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017 17
  18. 18. 2027 • Production mode for GACS releases (new terms, concept, mappings added with clear procedures, curation, validation, endorsement) • Alike the UMLS releases • Second used of data enabled by semantic interoperability, data mining and AI • Knowledge, knowledge, knowledge… 18AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017
  19. 19. AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017 19
  20. 20. AgroPortal - eRosa stakeholder workshop - Montpellier, July 6th 2017 20 Where is agriculture? NCBO BioPortal data as of 2013

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